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Xrcc4 X-ray repair cross complementing 4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 309995, updated on 10-Jul-2024

Summary

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Official Symbol
Xrcc4provided by RGD
Official Full Name
X-ray repair cross complementing 4provided by RGD
Primary source
RGD:1359573
See related
EnsemblRapid:ENSRNOG00000029966 AllianceGenome:RGD:1359573
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable FHA domain binding activity; identical protein binding activity; and protein C-terminus binding activity. Predicted to contribute to 3' overhang single-stranded DNA endodeoxyribonuclease activity. Involved in cellular response to lithium ion. Predicted to be located in chromosome, telomeric region; cytosol; and nucleoplasm. Predicted to be part of DNA ligase IV complex; DNA-dependent protein kinase-DNA ligase 4 complex; and ERCC4-ERCC1 complex. Predicted to be active in cytoplasm; nucleus; and site of double-strand break. Human ortholog(s) of this gene implicated in multiple myeloma. Orthologous to human XRCC4 (X-ray repair cross complementing 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 28.4), Heart (RPKM 22.4) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Xrcc4 in Genome Data Viewer
Location:
2q12
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (22686506..22932929, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (20948464..21197705, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (18674496..18927463, complement)

Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene versican Neighboring gene uncharacterized LOC134485711 Neighboring gene 40S ribosomal protein S6 pseudogene Neighboring gene small nucleolar RNA U109 Neighboring gene transmembrane protein 167A Neighboring gene uncharacterized LOC134485712

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Cloning, localization and focus formation at DNA damage sites of canine XRCC4. Koike M, et al. J Vet Med Sci, 2017 Jan 10. PMID 27644316, Free PMC Article
  2. XLF regulates filament architecture of the XRCC4·ligase IV complex. Hammel M, et al. Structure, 2010 Nov 10. PMID 21070942, Free PMC Article
  3. Lithium chloride protects retinal neurocytes from nutrient deprivation by promoting DNA non-homologous end-joining. Zhuang J, et al. Biochem Biophys Res Commun, 2009 Mar 13. PMID 19285016
  4. Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining. Ropars V, et al. Proc Natl Acad Sci U S A, 2011 Aug 2. PMID 21768349, Free PMC Article
  5. Requirement for XRCC4 and DNA ligase IV in alignment-based gap filling for nonhomologous DNA end joining in vitro. Lee JW, et al. Cancer Res, 2003 Jan 1. PMID 12517771

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Clone Names

  • MGC95022

Gene Ontology Provided by RGD

Function Evidence Code Pubs
contributes_to 3' overhang single-stranded DNA endodeoxyribonuclease activity ISO
Inferred from Sequence Orthology
more info
  
NOT enables DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables FHA domain binding ISO
Inferred from Sequence Orthology
more info
  
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
NOT enables ligase activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DN2 thymocyte differentiation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within DNA ligation ISO
Inferred from Sequence Orthology
more info
  
involved_in DNA ligation involved in DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA ligation involved in DNA repair ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within V(D)J recombination ISO
Inferred from Sequence Orthology
more info
  
involved_in cellular response to lithium ion IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within central nervous system development ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within double-strand break repair ISO
Inferred from Sequence Orthology
more info
  
involved_in double-strand break repair ISO
Inferred from Sequence Orthology
more info
  
involved_in double-strand break repair via nonhomologous end joining IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
  
involved_in double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of fibroblast proliferation ISO
Inferred from Sequence Orthology
more info
  
involved_in immunoglobulin V(D)J recombination IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within immunoglobulin V(D)J recombination ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within in utero embryonic development ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within isotype switching ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within negative regulation of neuron apoptotic process ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of protection from non-homologous end joining at telomere ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of neurogenesis ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of neuron apoptotic process ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within positive regulation of fibroblast proliferation ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within positive regulation of neurogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of phosphatidylserine exposure on apoptotic cell surface ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within pro-B cell differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization to site of double-strand break ISO
Inferred from Sequence Orthology
more info
  
involved_in response to X-ray IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within response to X-ray ISO
Inferred from Sequence Orthology
more info
  
involved_in response to X-ray ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within response to gamma radiation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within response to ionizing radiation ISO
Inferred from Sequence Orthology
more info
  
involved_in telomeric DNA-containing double minutes formation ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of DNA ligase IV complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of DNA ligase IV complex ISO
Inferred from Sequence Orthology
more info
  
part_of DNA-dependent protein kinase-DNA ligase 4 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of DNA-dependent protein kinase-DNA ligase 4 complex ISO
Inferred from Sequence Orthology
more info
  
part_of ERCC4-ERCC1 complex ISO
Inferred from Sequence Orthology
more info
  
located_in chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
  
NOT located_in condensed chromosome ISO
Inferred from Sequence Orthology
more info
  
is_active_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
part_of nonhomologous end joining complex ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
is_active_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
  
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
DNA repair protein XRCC4
Names
X-ray repair complementing defective repair in Chinese hamster cells 4
X-ray repair cross complementing protein 4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001006999.1 → NP_001007000.1  DNA repair protein XRCC4

    See identical proteins and their annotated locations for NP_001007000.1

    Status: PROVISIONAL

    Source sequence(s)
    BC083848
    UniProtKB/TrEMBL
    A0A8I6A2T0, A6I4N6, F7EEB9, Q5XI44
    Related
    ENSRNOP00000048754.4, ENSRNOT00000045850.4
    Conserved Domains (1) summary
    pfam06632
    Location:2 → 323
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086020.1 Reference GRCr8

    Range
    22686506..22932929 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_008760636.3 → XP_008758858.1  DNA repair protein XRCC4 isoform X1

    See identical proteins and their annotated locations for XP_008758858.1

    UniProtKB/TrEMBL
    F7EEB9
    Conserved Domains (1) summary
    pfam06632
    Location:2 → 334
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

  2. XM_006231751.4 → XP_006231813.1  DNA repair protein XRCC4 isoform X2

    See identical proteins and their annotated locations for XP_006231813.1

    UniProtKB/TrEMBL
    A0A8I6A2T0, A6I4N6, F7EEB9, Q5XI44
    Conserved Domains (1) summary
    pfam06632
    Location:2 → 323
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

  3. XM_008760637.4 → XP_008758859.1  DNA repair protein XRCC4 isoform X1

    See identical proteins and their annotated locations for XP_008758859.1

    UniProtKB/TrEMBL
    F7EEB9
    Conserved Domains (1) summary
    pfam06632
    Location:2 → 334
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

  4. XM_063281711.1 → XP_063137781.1  DNA repair protein XRCC4 isoform X2

    UniProtKB/TrEMBL
    A0A8I6A2T0, A6I4N6, F7EEB9, Q5XI44

  5. XM_039102166.2 → XP_038958094.1  DNA repair protein XRCC4 isoform X1

    UniProtKB/TrEMBL
    F7EEB9
    Conserved Domains (1) summary
    pfam06632
    Location:2 → 334
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

  6. XM_063281710.1 → XP_063137780.1  DNA repair protein XRCC4 isoform X2

    UniProtKB/TrEMBL
    A0A8I6A2T0, A6I4N6, F7EEB9, Q5XI44

  7. XM_039102165.2 → XP_038958093.1  DNA repair protein XRCC4 isoform X1

    UniProtKB/TrEMBL
    F7EEB9
    Conserved Domains (1) summary
    pfam06632
    Location:2 → 334
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

  8. XM_039102168.2 → XP_038958096.1  DNA repair protein XRCC4 isoform X2

    UniProtKB/TrEMBL
    A0A8I6A2T0, A6I4N6, F7EEB9, Q5XI44
    Related
    ENSRNOP00000085204.2, ENSRNOT00000097360.2
    Conserved Domains (1) summary
    pfam06632
    Location:2 → 323
    XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

  9. XM_063281713.1 → XP_063137783.1  DNA repair protein XRCC4 isoform X4

  10. XM_063281712.1 → XP_063137782.1  DNA repair protein XRCC4 isoform X3

  11. XM_063281714.1 → XP_063137784.1  DNA repair protein XRCC4 isoform X4

Nucleotide Protein Strain
Heading Accession and Version

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